/static/scripts/mvc/collection/paired-collection-creator.js

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define([
    "utils/levenshtein",
    "mvc/base-mvc",
    "utils/localization"
], function( levelshteinDistance, baseMVC, _l ){
//=============================================================================
/** An interface for building collections of paired datasets.
 */
var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({

    className: 'collection-creator flex-row-container',

    /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */
    initialize : function( attributes ){
        //console.debug( '-- PairedCollectionCreator:', attributes );

        attributes = _.defaults( attributes, {
            datasets            : [],
            filters             : this.DEFAULT_FILTERS,
            automaticallyPair   : true,
            matchPercentage     : 1.0,
            //matchPercentage     : 0.9,
            //matchPercentage     : 0.8,
            //strategy            : 'levenshtein'
            strategy            : 'lcs'
        });
        //console.debug( 'attributes now:', attributes );

        /** unordered, original list */
        this.initialList = attributes.datasets;

        /** is this from a history? if so, what's its id? */
        this.historyId = attributes.historyId;

        /** which filters should be used initially? (String[2] or name in commonFilters) */
        this.filters = this.commonFilters[ attributes.filters ] || this.commonFilters[ this.DEFAULT_FILTERS ];
        if( _.isArray( attributes.filters ) ){
            this.filters = attributes.filters;
        }

        /** try to auto pair the unpaired datasets on load? */
        this.automaticallyPair = attributes.automaticallyPair;

        /** distance/mismatch level allowed for autopairing */
        this.matchPercentage = attributes.matchPercentage;

        /** what method to use for auto pairing (will be passed aggression level) */
        this.strategy = this.strategies[ attributes.strategy ] || this.strategies[ this.DEFAULT_STRATEGY ];
        if( _.isFunction( attributes.strategy ) ){
            this.strategy = attributes.strategy;
        }

        /** remove file extensions (\.*) from created pair names? */
        this.removeExtensions = true;
        //this.removeExtensions = false;

        /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */
        this.oncancel = attributes.oncancel;
        /** fn to call when the collection is created (scoped to this) */
        this.oncreate = attributes.oncreate;

        /** is the unpaired panel shown? */
        this.unpairedPanelHidden = false;
        /** is the paired panel shown? */
        this.pairedPanelHidden = false;

        this._dataSetUp();

        this._setUpBehaviors();
    },

    /** map of common filter pairs by name */
    commonFilters : {
        none            : [ '', '' ],
        illumina        : [ '_1', '_2' ]
    },
    /** which commonFilter to use by default */
    DEFAULT_FILTERS : 'illumina',
    //DEFAULT_FILTERS : 'none',

    /** map of name->fn for autopairing */
    strategies : {
        'lcs'           : 'autoPairLCSs',
        'levenshtein'   : 'autoPairLevenshtein'
    },
    /** default autopair strategy name */
    DEFAULT_STRATEGY : 'lcs',

    // ------------------------------------------------------------------------ process raw list
    /** set up main data: cache initialList, sort, and autopair */
    _dataSetUp : function(){
        //console.debug( '-- _dataSetUp' );

        this.paired = [];
        this.unpaired = [];

        //this.fwdSelectedIds = [];
        //this.revSelectedIds = [];
        this.selectedIds = [];

        // sort initial list, add ids if needed, and save new working copy to unpaired
        this._sortInitialList();
        this._ensureIds();
        this.unpaired = this.initialList.slice( 0 );

        if( this.automaticallyPair ){
            this.autoPair();
        }
    },

    /** sort initial list */
    _sortInitialList : function(){
        //console.debug( '-- _sortInitialList' );
        this._sortDatasetList( this.initialList );
        //this._printList( this.unpaired );
    },

    /** sort a list of datasets */
    _sortDatasetList : function( list ){
        // currently only natural sort by name
        list.sort( function( a, b ){ return naturalSort( a.name, b.name ); });
        return list;
    },

    /** add ids to dataset objs in initial list if none */
    _ensureIds : function(){
        this.initialList.forEach( function( dataset ){
            if( !dataset.hasOwnProperty( 'id' ) ){
                dataset.id = _.uniqueId();
            }
        });
        //this._printList( this.unpaired );
        return this.initialList;
    },

    /** split initial list into two lists, those that pass forward filters & those passing reverse */
    _splitByFilters : function( filters ){
        var fwd = [],
            rev = [];
        this.unpaired.forEach( function( unpaired ){
            if( this._filterFwdFn( unpaired ) ){
                fwd.push( unpaired );
            }
            if( this._filterRevFn( unpaired ) ){
                rev.push( unpaired );
            }
        }.bind( this ) );
        return [ fwd, rev ];
    },

    /** filter fn to apply to forward datasets */
    _filterFwdFn : function( dataset ){
//TODO: this treats *all* strings as regex which may confuse people
        var regexp = new RegExp( this.filters[0] );
        return regexp.test( dataset.name );
        //return dataset.name.indexOf( this.filters[0] ) >= 0;
    },

    /** filter fn to apply to reverse datasets */
    _filterRevFn : function( dataset ){
        var regexp = new RegExp( this.filters[1] );
        return regexp.test( dataset.name );
    },

    /** add a dataset to the unpaired list in it's proper order */
    _addToUnpaired : function( dataset ){
        // currently, unpaired is natural sorted by name, use binary search to find insertion point
        var binSearchSortedIndex = function( low, hi ){
            if( low === hi ){ return low; }

            var mid = Math.floor( ( hi - low ) / 2 ) + low,
                compared = naturalSort( dataset.name, this.unpaired[ mid ].name );

            if( compared < 0 ){
                return binSearchSortedIndex( low, mid );
            } else if( compared > 0 ){
                return binSearchSortedIndex( mid + 1, hi );
            }
            // walk the equal to find the last
            while( this.unpaired[ mid ] && this.unpaired[ mid ].name === dataset.name ){ mid++; }
            return mid;

        }.bind( this );

        this.unpaired.splice( binSearchSortedIndex( 0, this.unpaired.length ), 0, dataset );
    },

    // ------------------------------------------------------------------------ auto pairing
//TODO: lots of boiler plate btwn the three auto pair fns
    /** two passes to automatically create pairs:
     *  use both simpleAutoPair, then the fn mentioned in strategy
     */
    autoPair : function( strategy ){
        strategy = strategy || this.strategy;
        //console.debug( '-- autoPair', strategy );
        this.simpleAutoPair();
        return this[ strategy ].call( this );
    },

    /** attempts to pair forward with reverse when names exactly match (after removing filters) */
    simpleAutoPair : function(){
        //console.debug( '-- simpleAutoPair' );
        // simplified auto pair that moves down unpaired lists *in order*,
        //  removes filters' strings from fwd and rev,
        //  and, if names w/o filters *exactly* match, creates a pair
        // possibly good as a first pass
        var i = 0, j,
            split = this._splitByFilters(),
            fwdList = split[0],
            revList = split[1],
            fwdName, revName,
            matchFound = false;

        while( i<fwdList.length ){
            var fwd = fwdList[ i ];
            //TODO: go through the filterFwdFn
            fwdName = fwd.name.replace( this.filters[0], '' );
            //console.debug( i, 'fwd:', fwdName );
            matchFound = false;

            for( j=0; j<revList.length; j++ ){
                var rev = revList[ j ];
                revName = rev.name.replace( this.filters[1], '' );
                //console.debug( '\t ', j, 'rev:', revName );

                if( fwd !== rev && fwdName === revName ){
                    matchFound = true;
                    // if it is a match, keep i at current, pop fwd, pop rev and break
                    //console.debug( '---->', fwdName, revName );
                    this._pair(
                        fwdList.splice( i, 1 )[0],
                        revList.splice( j, 1 )[0],
                        { silent: true }
                    );
                    break;
                }
            }
            if( !matchFound ){ i += 1; }
        }
        //console.debug( 'remaining Forward:' );
        //this._printList( this.unpairedForward );
        //console.debug( 'remaining Reverse:' );
        //this._printList( this.unpairedReverse );
        //console.debug( '' );
    },

    /** attempt to autopair using edit distance between forward and reverse (after removing filters) */
    autoPairLevenshtein : function(){
        //precondition: filters are set, both lists are not empty, and all filenames.length > filters[?].length
        //console.debug( '-- autoPairLevenshtein' );
        var i = 0, j,
            split = this._splitByFilters(),
            fwdList = split[0],
            revList = split[1],
            fwdName, revName,
            distance, bestIndex, bestDist;

        while( i<fwdList.length ){
            var fwd = fwdList[ i ];
            //TODO: go through the filterFwdFn
            fwdName = fwd.name.replace( this.filters[0], '' );
            //console.debug( i, 'fwd:', fwdName );
            bestDist = Number.MAX_VALUE;

            for( j=0; j<revList.length; j++ ){
                var rev = revList[ j ];
                revName = rev.name.replace( this.filters[1], '' );
                //console.debug( '\t ', j, 'rev:', revName );

                if( fwd !== rev ){
                    if( fwdName === revName ){
                        //console.debug( '\t\t exactmatch:', fwdName, revName );
                        bestIndex = j;
                        bestDist = 0;
                        break;
                    }
                    distance = levenshteinDistance( fwdName, revName );
                    //console.debug( '\t\t distance:', distance, 'bestDist:', bestDist );
                    if( distance < bestDist ){
                        bestIndex = j;
                        bestDist = distance;
                    }
                }
            }
            //console.debug( '---->', fwd.name, bestIndex, bestDist );
            //console.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist );

            var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) );
            //console.debug( '----> %', percentage * 100 );

            if( percentage >= this.matchPercentage ){
                this._pair(
                    fwdList.splice( i, 1 )[0],
                    revList.splice( bestIndex, 1 )[0],
                    { silent: true }
                );
                if( fwdList.length <= 0 || revList.length <= 0 ){
                    return;
                }
            } else {
                i += 1;
            }
        }
        //console.debug( 'remaining Forward:' );
        //this._printList( this.unpairedForward );
        //console.debug( 'remaining Reverse:' );
        //this._printList( this.unpairedReverse );
        //console.debug( '' );
    },

    /** attempt to auto pair using common substrings from both front and back (after removing filters) */
    autoPairLCSs : function(){
        //precondition: filters are set, both lists are not empty
        //console.debug( '-- autoPairLCSs' );
        var i = 0, j,
            split = this._splitByFilters(),
            fwdList = split[0],
            revList = split[1],
            fwdName, revName,
            currMatch, bestIndex, bestMatch;
        if( !fwdList.length || !revList.length ){ return; }
        //console.debug( fwdList, revList );

        while( i<fwdList.length ){
            var fwd = fwdList[ i ];
            fwdName = fwd.name.replace( this.filters[0], '' );
            //console.debug( i, 'fwd:', fwdName );
            bestMatch = 0;

            for( j=0; j<revList.length; j++ ){
                var rev = revList[ j ];
                revName = rev.name.replace( this.filters[1], '' );
                //console.debug( '\t ', j, 'rev:', revName );

                if( fwd !== rev ){
                    if( fwdName === revName ){
                        //console.debug( '\t\t exactmatch:', fwdName, revName );
                        bestIndex = j;
                        bestMatch = fwdName.length;
                        break;
                    }
                    var match = this._naiveStartingAndEndingLCS( fwdName, revName );
                    currMatch = match.length;
                    //console.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch );
                    if( currMatch > bestMatch ){
                        bestIndex = j;
                        bestMatch = currMatch;
                    }
                }
            }
            //console.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch );

            var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) );
            //console.debug( '----> %', percentage * 100 );

            if( percentage >= this.matchPercentage ){
                this._pair(
                    fwdList.splice( i, 1 )[0],
                    revList.splice( bestIndex, 1 )[0],
                    { silent: true }
                );
                if( fwdList.length <= 0 || revList.length <= 0 ){
                    return;
                }
            } else {
                i += 1;
            }
        }
        //console.debug( 'remaining Forward:' );
        //this._printList( this.unpairedForward );
        //console.debug( 'remaining Reverse:' );
        //this._printList( this.unpairedReverse );
        //console.debug( '' );
    },

    /** return the concat'd longest common prefix and suffix from two strings */
    _naiveStartingAndEndingLCS : function( s1, s2 ){
        var fwdLCS = '',
            revLCS = '',
            i = 0, j = 0;
        while( i < s1.length && i < s2.length ){
            if( s1[ i ] !== s2[ i ] ){
                break;
            }
            fwdLCS += s1[ i ];
            i += 1;
        }
        if( i === s1.length ){ return s1; }
        if( i === s2.length ){ return s2; }

        i = ( s1.length - 1 );
        j = ( s2.length - 1 );
        while( i >= 0 && j >= 0 ){
            if( s1[ i ] !== s2[ j ] ){
                break;
            }
            revLCS = [ s1[ i ], revLCS ].join( '' );
            i -= 1;
            j -= 1;
        }
        return fwdLCS + revLCS;
    },

    // ------------------------------------------------------------------------ pairing / unpairing
    /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */
    _pair : function( fwd, rev, options ){
        options = options || {};
        //TODO: eventing, options
        //console.debug( '_pair:', fwd, rev );
        var pair = this._createPair( fwd, rev, options.name );
        this.paired.push( pair );
        this.unpaired = _.without( this.unpaired, fwd, rev );
        if( !options.silent ){
            this.trigger( 'pair:new', pair );
        }
        return pair;
    },

    /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */
    _createPair : function( fwd, rev, name ){
        // ensure existance and don't pair something with itself
        if( !( fwd && rev ) || ( fwd === rev ) ){
            throw new Error( 'Bad pairing: ' + [ JSON.stringify( fwd ), JSON.stringify( rev ) ] );
        }
        name = name || this._guessNameForPair( fwd, rev );
        return { forward : fwd, name : name, reverse : rev };
    },

    /** try to find a good pair name for the given fwd and rev datasets */
    _guessNameForPair : function( fwd, rev, removeExtensions ){
        removeExtensions = ( removeExtensions !== undefined )?( removeExtensions ):( this.removeExtensions );
        var lcs = this._naiveStartingAndEndingLCS(
//TODO: won't work with regex
            fwd.name.replace( this.filters[0], '' ),
            rev.name.replace( this.filters[1], '' )
        );
        if( removeExtensions ){
            var lastDotIndex = lcs.lastIndexOf( '.' );
            if( lastDotIndex > 0 ){
                lcs = lcs.slice( 0, lastDotIndex );
            }
        }
        //TODO: optionally remove extension
        return lcs || ( fwd.name + ' & ' + rev.name );
    },

    ///** find datasets with fwdId and revID and pair them */
    //_pairById : function( fwdId, revId, name ){
    //    var both = this.unpaired.filter( function( unpaired ){
    //            return unpaired.id === fwdId || unpaired.id === revId;
    //        }),
    //        fwd = both[0], rev = both[1];
    //    if( both[0].id === revId ){
    //        fwd = rev; rev = both[0];
    //    }
    //    return this._pair( fwd, rev, name );
    //},

    /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */
    _unpair : function( pair, options ){
        options = options || {};
        if( !pair ){
            throw new Error( 'Bad pair: ' + JSON.stringify( pair ) );
        }
        this.paired = _.without( this.paired, pair );
        this._addToUnpaired( pair.forward );
        this._addToUnpaired( pair.reverse );

        if( !options.silent ){
            this.trigger( 'pair:unpair', [ pair ] );
        }
        return pair;
    },

    /** unpair all paired datasets */
    unpairAll : function(){
        var pairs = [];
        while( this.paired.length ){
            pairs.push( this._unpair( this.paired[ 0 ], { silent: true }) );
        }
        this.trigger( 'pair:unpair', pairs );
    },

    // ------------------------------------------------------------------------ API
    /** convert a pair into JSON compatible with the collections API */
    _pairToJSON : function( pair ){
        //TODO: consider making this the pair structure when created instead
        return {
            collection_type : 'paired',
            src             : 'new_collection',
            name            : pair.name,
            element_identifiers : [{
                name    : 'forward',
                id      : pair.forward.id,
                //TODO: isn't necessarily true
                src     : 'hda'
            }, {
                name    : 'reverse',
                id      : pair.reverse.id,
                //TODO: isn't necessarily true
                src     : 'hda'
            }]
        };
    },

    /** create the collection via the API
     *  @returns {jQuery.xhr Object}    the jquery ajax request
     */
    createList : function(){
        var creator = this,
            url;
        if( creator.historyId ){
            url = '/api/histories/' + this.historyId + '/contents/dataset_collections';
        //} else {
        //
        }

//TODO:?? Can't we use ListPairedCollection.create()
        var ajaxData = {
            type            : 'dataset_collection',
            collection_type : 'list:paired',
            name            : _.escape( creator.$( '.collection-name' ).val() ),
            element_identifiers : creator.paired.map( function( pair ){
                return creator._pairToJSON( pair );
            })
        };
        //console.debug( JSON.stringify( ajaxData ) );
        return jQuery.ajax( url, {
            type        : 'POST',
            contentType : 'application/json',
            dataType    : 'json',
            data        : JSON.stringify( ajaxData )
        })
        .fail( function( xhr, status, message ){
            creator._ajaxErrHandler( xhr, status, message );
        })
        .done( function( response, message, xhr ){
            //console.info( 'ok', response, message, xhr );
            creator.trigger( 'collection:created', response, message, xhr );
            if( typeof creator.oncreate === 'function' ){
                creator.oncreate.call( this, response, message, xhr );
            }
        });
    },

    /** handle ajax errors with feedback and details to the user (if available) */
    _ajaxErrHandler : function( xhr, status, message ){
        console.error( xhr, status, message );
        var content = _l( 'An error occurred while creating this collection' );
        if( xhr ){
            if( xhr.readyState === 0 && xhr.status === 0 ){
                content += ': ' + _l( 'Galaxy could not be reached and may be updating.' )
                    + _l( ' Try again in a few minutes.' );
            } else if( xhr.responseJSON ){
                content += '<br /><pre>' + JSON.stringify( xhr.responseJSON ) + '</pre>';
            } else {
                content += ': ' + message;
            }
        }
        creator._showAlert( content, 'alert-danger' );
    },

    // ------------------------------------------------------------------------ rendering
    /** render the entire interface */
    render : function( speed, callback ){
        //console.debug( '-- _render' );
        //this.$el.empty().html( PairedCollectionCreator.templates.main() );
        this.$el.empty().html( PairedCollectionCreator.templates.main() );
        this._renderHeader( speed );
        this._renderMiddle( speed );
        this._renderFooter( speed );
        this._addPluginComponents();
        return this;
    },

    /** render the header section */
    _renderHeader : function( speed, callback ){
        //console.debug( '-- _renderHeader' );
        var $header = this.$( '.header' ).empty().html( PairedCollectionCreator.templates.header() )
            .find( '.help-content' ).prepend( $( PairedCollectionCreator.templates.helpContent() ) );

        this._renderFilters();
        return $header;
    },
    /** fill the filter inputs with the filter values */
    _renderFilters : function(){
        return    this.$( '.forward-column .column-header input' ).val( this.filters[0] )
            .add( this.$( '.reverse-column .column-header input' ).val( this.filters[1] ) );
    },

    /** render the middle including unpaired and paired sections (which may be hidden) */
    _renderMiddle : function( speed, callback ){
        var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() );

        // (re-) hide the un/paired panels based on instance vars
        //TODO: use replaceWith
        if( this.unpairedPanelHidden ){
            this.$( '.unpaired-columns' ).hide();
        } else if( this.pairedPanelHidden ){
            this.$( '.paired-columns' ).hide();
        }

        this._renderUnpaired();
        this._renderPaired();
        return $middle;
    },
    /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */
    _renderUnpaired : function( speed, callback ){
        //console.debug( '-- _renderUnpaired' );
        var creator = this,
            $fwd, $rev, $prd = [],
            split = this._splitByFilters();
        // update unpaired counts
        this.$( '.forward-column .title' )
            .text([ split[0].length, _l( 'unpaired forward' ) ].join( ' ' ));
        this.$( '.forward-column .unpaired-info' )
            .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[0].length ) );
        this.$( '.reverse-column .title' )
            .text([ split[1].length, _l( 'unpaired reverse' ) ].join( ' ' ));
        this.$( '.reverse-column .unpaired-info' )
            .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[1].length ) );

        // show/hide the auto pair button if any unpaired are left
        this.$( '.autopair-link' ).toggle( this.unpaired.length !== 0 );
        if( this.unpaired.length === 0 ){
            this._renderUnpairedEmpty();
            //this.$( '.unpaired-columns .paired-column .column-datasets' )
            //    .append( this._renderUnpairedEmpty() );
            //TODO: would be best to return here (the $columns)
            return;
        }

        // create the dataset dom arrays
        $rev = split[1].map( function( dataset, i ){
            // if there'll be a fwd dataset across the way, add a button to pair the row
            if( ( split[0][ i ] !== undefined )
            &&  ( split[0][ i ] !== dataset ) ){
                $prd.push( creator._renderPairButton() );
            }
            return creator._renderUnpairedDataset( dataset );
        });
        $fwd = split[0].map( function( dataset ){
            return creator._renderUnpairedDataset( dataset );
        });

        if( !$fwd.length && !$rev.length ){
            this._renderUnpairedNotShown();
            return;
        }
        // add to appropo cols
        //TODO: not the best way to render
        this.$( '.unpaired-columns .column-datasets' ).empty();
        this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd )
            .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) )
            .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) );
    },
    /** return a string to display the count of filtered out datasets */
    _renderUnpairedDisplayStr : function( numFiltered ){
        return [ '(', numFiltered, ' ', _l( 'filtered out' ), ')' ].join('');
    },
    /** return an unattached jQuery DOM element to represent an unpaired dataset */
    _renderUnpairedDataset : function( dataset ){
        //TODO: to underscore template
        return $( '<li/>')
            .attr( 'id', 'dataset-' + dataset.id )
            .addClass( 'dataset unpaired' )
            .attr( 'draggable', true )
            .addClass( dataset.selected? 'selected': '' )
            .append( $( '<span/>' ).addClass( 'dataset-name' ).text( dataset.name ) )
            //??
            .data( 'dataset', dataset );
    },
    /** render the button that may go between unpaired datasets, allowing the user to pair a row */
    _renderPairButton : function(){
        //TODO: *not* a dataset - don't pretend like it is
        return $( '<li/>').addClass( 'dataset unpaired' )
            .append( $( '<span/>' ).addClass( 'dataset-name' ).text( _l( 'Pair these datasets' ) ) );
    },
    /** a message to display when no unpaired left */
    _renderUnpairedEmpty : function(){
        //console.debug( '-- renderUnpairedEmpty' );
        var $msg = $( '<div class="empty-message"></div>' )
            .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' );
        this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );
        return $msg;
    },
    /** a message to display when no unpaired can be shown with the current filters */
    _renderUnpairedNotShown : function(){
        //console.debug( '-- renderUnpairedEmpty' );
        var $msg = $( '<div class="empty-message"></div>' )
            .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' );
        this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg );
        return $msg;
    },

    /** render the paired section and update counts of paired datasets */
    _renderPaired : function( speed, callback ){
        //console.debug( '-- _renderPaired' );
        var $fwd = [],
            $prd = [],
            $rev = [];

        this.$( '.paired-column-title .title' ).text([ this.paired.length, _l( 'paired' ) ].join( ' ' ) );
        // show/hide the unpair all link
        this.$( '.unpair-all-link' ).toggle( this.paired.length !== 0 );
        if( this.paired.length === 0 ){
            this._renderPairedEmpty();
            //TODO: would be best to return here (the $columns)
        } else {
            // show/hide 'remove extensions link' when any paired and they seem to have extensions
            this.$( '.remove-extensions-link' ).show();
        }

        this.paired.forEach( function( pair, i ){
            $fwd.push( $( '<li/>').addClass( 'dataset paired' )
                .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.forward.name ) ) );
            $prd.push( $( '<li/>').addClass( 'dataset paired' )
                .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.name ) ) );
            $rev.push( $( '<li/>').addClass( 'dataset paired' )
                .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.reverse.name ) ) );
            $rev.push( $( '<button/>' ).addClass( 'unpair-btn' )
                .append( $( '<span/>' ).addClass( 'fa fa-unlink' ).attr( 'title', _l( 'Unpair' ) ) ) );
        });

        //TODO: better as one swell foop (instead of 4 repaints)
        this.$( '.paired-columns .column-datasets' ).empty();
        return    this.$( '.paired-columns .forward-column .column-datasets' ).prepend( $fwd )
            .add( this.$( '.paired-columns .paired-column .column-datasets' ).prepend( $prd ) )
            .add( this.$( '.paired-columns .reverse-column .column-datasets' ).prepend( $rev ) );
    },
    /** a message to display when none paired */
    _renderPairedEmpty : function(){
        var $msg = $( '<div class="empty-message"></div>' )
            .text( '(' + _l( 'no paired datasets yet' ) + ')' );
        this.$( '.paired-columns .paired-column .column-datasets' ).prepend( $msg );
        return $msg;
    },

    /** render the footer, completion controls, and cancel controls */
    _renderFooter : function( speed, callback ){
        var $footer = this.$( '.footer' ).empty().html( PairedCollectionCreator.templates.footer() );
        this.$( '.remove-extensions' ).prop( 'checked', this.removeExtensions );
        if( typeof this.oncancel === 'function' ){
            this.$( '.cancel-create.btn' ).show();
        }
        return $footer;
    },

    /** add any jQuery/bootstrap/custom plugins to elements rendered */
    _addPluginComponents : function(){
        this._chooseFiltersPopover( '.choose-filters-link' );
        this.$( '.help-content i' ).hoverhighlight( '.collection-creator', 'rgba( 192, 255, 255, 1.0 )' );
    },

    /** build a filter selection popover allowing selection of common filter pairs */
    _chooseFiltersPopover : function( selector ){
        function filterChoice( val1, val2 ){
            return [
                '<button class="filter-choice btn" ',
                        'data-forward="', val1, '" data-reverse="', val2, '">',
                    _l( 'Forward' ), ': ', val1, ', ',
                    _l( 'Reverse' ), ': ', val2,
                '</button>'
            ].join('');
        }
        var $popoverContent = $( _.template([
            '<div class="choose-filters">',
                '<div class="help">',
                    _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ),
                ':</div>',
                //TODO: connect with common filters
                filterChoice( '_1', '_2' ),
                filterChoice( '_R1', '_R2' ),
            '</div>'
        ].join(''), {}));

        return this.$( selector ).popover({
            container   : '.collection-creator',
            placement   : 'bottom',
            html        : true,
            //animation   : false,
            content     : $popoverContent
        });
    },

    /** add (or clear if clear is truthy) a validation warning to what */
    _validationWarning : function( what, clear ){
        var VALIDATION_CLASS = 'validation-warning';
        if( what === 'name' ){
            what = this.$( '.collection-name' ).add( this.$( '.collection-name-prompt' ) );
            this.$( '.collection-name' ).focus().select();
        }
        if( clear ){
            what = what || this.$( '.' + VALIDATION_CLASS );
            what.removeClass( VALIDATION_CLASS );
        } else {
            what.addClass( VALIDATION_CLASS );
        }
    },
    
    // ------------------------------------------------------------------------ events
    /** set up event handlers on self */
    _setUpBehaviors : function(){
        this.on( 'pair:new', function(){
            //TODO: ideally only re-render the columns (or even elements) involved
            this._renderUnpaired();
            this._renderPaired();

            // scroll to bottom where new pairs are added
            //TODO: this doesn't seem to work - innerHeight sticks at 133...
            //  may have to do with improper flex columns
            //var $pairedView = this.$( '.paired-columns' );
            //$pairedView.scrollTop( $pairedView.innerHeight() );
            //console.debug( $pairedView.height() )
            this.$( '.paired-columns' ).scrollTop( 8000000 );
        });
        this.on( 'pair:unpair', function( pairs ){
            //TODO: ideally only re-render the columns (or even elements) involved
            this._renderUnpaired();
            this._renderPaired();
            this.splitView();
        });

        this.on( 'filter-change', function(){
            this.filters = [
                this.$( '.forward-unpaired-filter input' ).val(),
                this.$( '.reverse-unpaired-filter input' ).val()
            ];
            this._renderFilters();
            this._renderUnpaired();
        });

        this.on( 'autopair', function(){
            this._renderUnpaired();
            this._renderPaired();

            var message, msgClass = null;
            if( this.paired.length ){
                msgClass = 'alert-success';
                message = this.paired.length + ' ' + _l( 'pairs created' );
                if( !this.unpaired.length ){
                    message += ': ' + _l( 'all datasets have been successfully paired' );
                    this.hideUnpaired();
                }
            } else {
                message = _l( 'Could not automatically create any pairs from the given dataset names' );
            }
            this._showAlert( message, msgClass );
        });

        //this.on( 'all', function(){
        //    console.info( arguments );
        //});
        return this;
    },

    events : {
        // header
        'click .more-help'                          : '_clickMoreHelp',
        'click .less-help'                          : '_clickLessHelp',
        'click .header .alert button'               : '_hideAlert',
        'click .forward-column .column-title'       : '_clickShowOnlyUnpaired',
        'click .reverse-column .column-title'       : '_clickShowOnlyUnpaired',
        'click .unpair-all-link'                    : '_clickUnpairAll',
        //TODO: this seems kinda backasswards
        'change .forward-unpaired-filter input'     : function( ev ){ this.trigger( 'filter-change' ); },
        'focus .forward-unpaired-filter input'      : function( ev ){ $( ev.currentTarget ).select(); },
        'click .autopair-link'                      : '_clickAutopair',
        'click .choose-filters .filter-choice'      : '_clickFilterChoice',
        'click .clear-filters-link'                 : '_clearFilters',
        'change .reverse-unpaired-filter input'     : function( ev ){ this.trigger( 'filter-change' ); },
        'focus .reverse-unpaired-filter input'      : function( ev ){ $( ev.currentTarget ).select(); },
        // unpaired
        'click .forward-column .dataset.unpaired'   : '_clickUnpairedDataset',
        'click .reverse-column .dataset.unpaired'   : '_clickUnpairedDataset',
        'click .paired-column .dataset.unpaired'    : '_clickPairRow',
        'click .unpaired-columns'                   : 'clearSelectedUnpaired',
        // divider
        'click .paired-column-title'                : '_clickShowOnlyPaired',
        'mousedown .flexible-partition-drag'        : '_startPartitionDrag',
        // paired
        'click .paired-columns .paired-column .dataset-name' : '_clickPairName',
        'mouseover .dataset.paired'                 : '_hoverPaired',
        'mouseout .dataset.paired'                  : '_hoverOutPaired',
        'click .unpair-btn'                         : '_clickUnpair',

        // footer
        'change .remove-extensions'                 : function( ev ){ this.toggleExtensions(); },
        'change .collection-name'                   : '_changeName',
        'click .cancel-create'                      : function( ev ){
            if( typeof this.oncancel === 'function' ){
                this.oncancel.call( this );
            }
        },
        'click .create-collection'                  : '_clickCreate'
    },

    // ........................................................................ header
    /** expand help */
    _clickMoreHelp : function( ev ){
        this.$( '.main-help' ).addClass( 'expanded' );
        this.$( '.more-help' ).hide();
    },
    /** collapse help */
    _clickLessHelp : function( ev ){
        this.$( '.main-help' ).removeClass( 'expanded' );
        this.$( '.more-help' ).show();
    },

    /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/
    _showAlert : function( message, alertClass ){
        alertClass = alertClass || 'alert-danger';
        this.$( '.main-help' ).hide();
        this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show()
            .find( '.alert-message' ).html( message );
    },
    /** hide the alerts at the top */
    _hideAlert : function( message ){
        this.$( '.main-help' ).show();
        this.$( '.header .alert' ).hide();
    },

    //TODO: consolidate these
    /** toggle between showing only unpaired and split view */
    _clickShowOnlyUnpaired : function( ev ){
        //console.debug( 'click unpaired', ev.currentTarget );
        if( this.$( '.paired-columns' ).is( ':visible' ) ){
            this.hidePaired();
        } else {
            this.splitView();
        }
    },
    /** toggle between showing only paired and split view */
    _clickShowOnlyPaired : function( ev ){
        //console.debug( 'click paired' );
        if( this.$( '.unpaired-columns' ).is( ':visible' ) ){
            this.hideUnpaired();
        } else {
            this.splitView();
        }
    },
    /** hide unpaired, show paired */
    hideUnpaired : function( speed, callback ){
        speed = speed || 0;
        this.$( '.unpaired-columns' ).hide( speed, callback );
        //this.$( '.unpaired-filter' ).hide( speed );
        this.$( '.paired-columns' ).show( speed ).css( 'flex', '1 0 auto' );
        this.unpairedPanelHidden = true;
    },
    /** hide paired, show unpaired */
    hidePaired : function( speed, callback ){
        speed = speed || 0;
        this.$( '.unpaired-columns' ).show( speed ).css( 'flex', '1 0 auto' );
        //this.$( '.unpaired-filter' ).show( speed );
        this.$( '.paired-columns' ).hide( speed, callback );
        this.pairedPanelHidden = true;
    },
    /** show both paired and unpaired (splitting evenly) */
    splitView : function( speed, callback ){
        speed = speed || 0;
        this.unpairedPanelHidden = this.pairedPanelHidden = false;
        //this.$( '.unpaired-filter' ).show( speed );
        this._renderMiddle( speed );
        return this;
    },

    /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */
    _clickUnpairAll : function( ev ){
        this.unpairAll();
    },

    /** attempt to autopair */
    _clickAutopair : function( ev ){
        var paired = this.autoPair();
        //console.debug( 'autopaired', paired );
        //TODO: an indication of how many pairs were found - if 0, assist
        this.trigger( 'autopair', paired );
    },

    /** set the filters based on the data attributes of the button click target */
    _clickFilterChoice : function( ev ){
        var $selected = $( ev.currentTarget );
        this.$( '.forward-unpaired-filter input' ).val( $selected.data( 'forward' ) );
        this.$( '.reverse-unpaired-filter input' ).val( $selected.data( 'reverse' ) );
        this._hideChooseFilters();
        this.trigger( 'filter-change' );
    },

    /** hide the choose filters popover */
    _hideChooseFilters : function(){
        //TODO: update bootstrap and remove the following hack
        //  see also: https://github.com/twbs/bootstrap/issues/10260
        this.$( '.choose-filters-link' ).popover( 'hide' );
        this.$( '.popover' ).css( 'display', 'none' );
    },

    /** clear both filters */
    _clearFilters : function( ev ){
        this.$( '.forward-unpaired-filter input' ).val( '' );
        this.$( '.reverse-unpaired-filter input' ).val( '' );
        this.trigger( 'filter-change' );
    },

    // ........................................................................ unpaired
    /** select an unpaired dataset */
    _clickUnpairedDataset : function( ev ){
        ev.stopPropagation();
        return this.toggleSelectUnpaired( $( ev.currentTarget ) );
    },

    /** Toggle the selection of an unpaired dataset representation.
     *  @param [jQuery] $dataset        the unpaired dataset dom rep to select
     *  @param [Boolean] options.force  if defined, force selection based on T/F; otherwise, toggle
     */
    toggleSelectUnpaired : function( $dataset, options ){
        options = options || {};
        var dataset = $dataset.data( 'dataset' ),
            select = options.force !== undefined? options.force: !$dataset.hasClass( 'selected' );
        //console.debug( id, options.force, $dataset, dataset );
        if( !$dataset.size() || dataset === undefined ){ return $dataset; }

        if( select ){
            $dataset.addClass( 'selected' );
            if( !options.waitToPair ){
                this.pairAllSelected();
            }

        } else {
            $dataset.removeClass( 'selected' );
            //delete dataset.selected;
        }
        return $dataset;
    },

    /** pair all the currently selected unpaired datasets */
    pairAllSelected : function( options ){
        options = options || {};
        var creator = this,
            fwds = [],
            revs = [],
            pairs = [];
        //TODO: could be made more concise
        creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){
            fwds.push( $( this ).data( 'dataset' ) );
        });
        creator.$( '.unpaired-columns .reverse-column .dataset.selected' ).each( function(){
            revs.push( $( this ).data( 'dataset' ) );
        });
        fwds.length = revs.length = Math.min( fwds.length, revs.length );
        //console.debug( fwds );
        //console.debug( revs );
        fwds.forEach( function( fwd, i ){
            try {
                pairs.push( creator._pair( fwd, revs[i], { silent: true }) );

            } catch( err ){
                //TODO: preserve selected state of those that couldn't be paired
                //TODO: warn that some could not be paired
                console.error( err );
            }
        });
        if( pairs.length && !options.silent ){
            this.trigger( 'pair:new', pairs );
        }
        return pairs;
    },

    /** clear the selection on all unpaired datasets */
    clearSelectedUnpaired : function(){
        this.$( '.unpaired-columns .dataset.selected' ).removeClass( 'selected' );
    },

    /** attempt to pair two datasets directly across from one another */
    _clickPairRow : function( ev ){
        //if( !ev.currentTarget ){ return true; }
        var rowIndex = $( ev.currentTarget ).index(),
            fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ),
            rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' );
        //console.debug( 'row:', rowIndex, fwd, rev );
        //TODO: animate
        this._pair( fwd, rev );
    },

    // ........................................................................ divider/partition
    /** start dragging the visible divider/partition between unpaired and paired panes */
    _startPartitionDrag : function( ev ){
        var creator = this,
            startingY = ev.pageY;
        //console.debug( 'partition drag START:', ev );
        $( 'body' ).css( 'cursor', 'ns-resize' );
        creator.$( '.flexible-partition-drag' ).css( 'color', 'black' );

        function endDrag( ev ){
            //console.debug( 'partition drag STOP:', ev );
            // doing this by an added class didn't really work well - kept flashing still
            creator.$( '.flexible-partition-drag' ).css( 'color', '' );
            $( 'body' ).css( 'cursor', '' ).unbind( 'mousemove', trackMouse );
        }
        function trackMouse( ev ){
            var offset = ev.pageY - startingY;
            if( !creator.adjPartition( offset ) ){
                $( 'body' ).trigger( 'mouseup' );
            }
            startingY += offset;
        }
        $( 'body' ).mousemove( trackMouse );
        $( 'body' ).one( 'mouseup', endDrag );
    },

    /** adjust the parition up/down +/-adj pixels */
    adjPartition : function( adj ){
        var $unpaired = this.$( '.unpaired-columns' ),
            $paired = this.$( '.paired-columns' ),
            unpairedHi = parseInt( $unpaired.css( 'height' ), 10 ),
            pairedHi = parseInt( $paired.css( 'height' ), 10 );
        //console.debug( adj, 'hi\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );

        unpairedHi = Math.max( 10, unpairedHi + adj );
        pairedHi = pairedHi - adj;

        if( unpairedHi <= 10 ){
            this.hideUnpaired();
            return false;
        } else if( !$unpaired.is( 'visible' ) ){
            $unpaired.show();
            //this.$( '.unpaired-filter' ).show();
        }

        if( pairedHi <= 15 ){
            this.hidePaired();
            if( pairedHi < 10 ){ return false; }

        } else if( !$paired.is( 'visible' ) ){
            $paired.show();
        }

        $unpaired.css({
            height  : unpairedHi + 'px',
            flex    : '0 0 auto'
        });
        return true;
    },

    // ........................................................................ paired
    /** rename a pair when the pair name is clicked */
    _clickPairName : function( ev ){
        var $control = $( ev.currentTarget ),
            pair = this.paired[ $control.parent().index() ],
            response = prompt( 'Enter a new name for the pair:', pair.name );
        if( response ){
            pair.name = response;
            // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these
            //  when adding/removing extensions
            //TODO: kinda hacky
            pair.customizedName = true;
            $control.text( pair.name );
        }
    },

    /** unpair this pair */
    _clickUnpair : function( ev ){
        //if( !ev.currentTarget ){ return true; }
        //TODO: this is a hack bc each paired rev now has two elems (dataset, button)
        var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 );
        //console.debug( 'pair:', pairIndex );
        //TODO: animate
        this._unpair( this.paired[ pairIndex ] );
    },

    //TODO: the following is ridiculous
    _hoverPaired : function( ev ){
        var $target = $( ev.currentTarget ),
            index = $target.index();
        //TODO: this is a hack bc each paired rev now has two elems (dataset, button)
        if( $target.parents( '.reverse-column' ).size() ){
            index = Math.floor( index / 2 );
        }
        //console.debug( 'index:', index );
        this.emphasizePair( index );
    },
    _hoverOutPaired : function( ev ){
        var $target = $( ev.currentTarget ),
            index = $target.index();
        //TODO: this is a hack bc each paired rev now has two elems (dataset, button)
        if( $target.parents( '.reverse-column' ).size() ){
            index = Math.floor( index / 2 );
        }
        //console.debug( 'index:', index );
        this.deemphasizePair( index );
    },
    emphasizePair : function( index ){
        //console.debug( 'emphasizePairedBorder:', index );
        this.$( '.paired-columns .forward-column .dataset.paired' ).eq( index )
            .add( this.$( '.paired-columns .paired-column .dataset.paired' ).eq( index ) )
            .add( this.$( '.paired-columns .reverse-column .dataset.paired' ).eq( index ) )
            .addClass( 'emphasized' );
    },
    deemphasizePair : function( index ){
        //console.debug( 'deemphasizePairedBorder:', index );
        this.$( '.paired-columns .forward-column .dataset.paired' ).eq( index )
            .add( this.$( '.paired-columns .paired-column .dataset.paired' ).eq( index ) )
            .add( this.$( '.paired-columns .reverse-column .dataset.paired' ).eq( index ) )
            .removeClass( 'emphasized' );
    },

    // ........................................................................ footer
    toggleExtensions : function( force ){
        var creator = this;
        creator.removeExtensions = ( force !== undefined )?( force ):( !creator.removeExtensions );

        _.each( creator.paired, function( pair ){
            // don't overwrite custom names
            if( pair.customizedName ){ return; }
            pair.name = creator._guessNameForPair( pair.forward, pair.reverse );
        });

  …

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